External files for distribution of molecular diagnostic tests and determination of compatibility between tests

ABSTRACT

Embodiments disclosed herein relate to methods and systems for performing an automated assay, and particularly to performing an assay on a plurality of samples on an automated instrument.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application claims priority to U.S. Provisional ApplicationSer. No. 61/594,867, entitled “EXTERNAL FILES FOR DISTRIBUTION OFMOLECULAR DIAGNOSTIC TESTS AND DETERMINATION OF COMPATIBILITY BETWEENTESTS,” filed Feb. 3, 2012, the entire disclosure of which is hereinincorporated by reference in its entirety

BACKGROUND OF THE INVENTION

1. Field of the Invention

Embodiments disclosed herein relate to methods and systems forperforming an automated assay, and particularly to performing aplurality of assays on a plurality of samples on an automatedinstrument.

2. Description of the Related Art

The medical diagnostics industry is a critical element of today'shealthcare infrastructure. In the last decade, the use of nucleic acidbased assays for diagnostic testing has become increasingly more common.The automation of processing and testing samples in diagnostic testingis appealing, as it minimizes experimental variability and reduces theneed for highly trained technicians. In addition to benefits in thefield of diagnostics, automation of processing and testing samples hasfacilitated high throughput testing.

Understanding that processing samples for purposes such as diagnostictesting or high throughput testing may break down into several keysteps, it is often desirable to automate one or more steps. For example,in the context of diagnostics, a biological sample, such as thoseobtained from a patient, can be used in nucleic acid amplificationassays in order to amplify a target nucleic acid (e.g., DNA, RNA, or thelike) of interest. Once amplified, the presence of a target nucleicacid, or amplification product of a target nucleic acid (e.g., a targetamplicon) can be detected, wherein the presence of a target nucleic acidand/or target amplicon is used to identify and/or quantify the presenceof a target (e.g., a target microorganism or the like). Often, nucleicacid amplification assays involve multiple steps, which can includenucleic acid extraction, nucleic acid amplification, and detection. Itis desirable to automate certain steps of these processes.

There is a need for improved methods and devices for carrying out assayson multiple samples in parallel. The embodiments described hereinaddress this need and can advantageously be used in clinical andresearch settings.

SUMMARY OF THE INVENTION

The present technology relates to methods and systems for performing anautomated assay, and particularly to performing a plurality of assays ona plurality of samples on an automated instrument. In some embodimentsof the present technology, such methods and systems can permit theconcurrent performance of discrete assay workflows on an instrument whenthe assay workflows are compatible, and can prevent the concurrentperformance of incompatible assays within the same workstation. Someembodiments relate to performing a plurality of user-defined protocols(UDP) on an automated instrument. Some embodiments relate to performinga plurality of assay definition files (ADF) developed by an assaymanufacturer. Some embodiments relate to performing one or more UDPs,optionally in combination with one or more ADFs, concurrently on thesame automated instrument.

In some embodiments of the technology presented herein, methods ofperforming an automated assay on a plurality of samples are providedthat allow for improved reliability and ease of use when performing anassay on an automated instrument. The methods can include providing anautomated instrument comprising a first workstation and a secondworkstation, each of the first and second workstations configured toreceive and processes a plurality of samples according to a plurality ofdifferent automated assay workflows, wherein each different automatedassay workflow has an associated unique assay definition or user-definedprotocol file; determining whether two discrete assay workflows arecompatible or incompatible with each other for concurrent processing onthe automated instrument; and performing the discrete assay workflowsconcurrently on the instrument when the assays are compatible.

In some embodiments, the assay definition or user defined protocol filecan comprise a first level compatibility index value, and wherein thedetermining step can comprise: (a) selecting a first assay from among afirst list of available assays; and (b) evaluating which of a pluralityof other available assays have an assay definition file comprising thesame first level compatibility index value as the first assay, whereinthe same first level compatibility index value is indicative offirst-level compatibility.

In some embodiments, the evaluating step can comprise (b1) identifyingany assays which have first level compatibility index values differentfrom the first compatibility index value of the first assay; and (b2)providing a second list of second assays, wherein the second listexcludes any assay having a first level compatibility index valuedifferent from the first compatibility index value of the first assay.

In some embodiments, each assay definition file can comprise a secondlevel compatibility index value, and wherein the determining stepfurther can comprise (c) evaluating which of a plurality of otheravailable assays have an assay definition file comprising the samesecond level compatibility index value as the first assay, wherein thesame second level compatibility index value is indicative ofsecond-level compatibility.

In some embodiments, the evaluating step can comprise (c1) identifyingany assays which have second level compatibility index values differentfrom the second compatibility index value of the first assay; and (c2)providing a second list of second assays, wherein the second listexcludes any assay having a second level compatibility index valuedifferent from the second compatibility index value of the first assay.

In some embodiments, the first level compatibility can comprisecompatibility of performing two assays concurrently at a singleworkstation, the parameters selected from the group consisting of:incubation time, lysis time, reagent volume, reagent type, incubationtemperature, lysis temperature, workstation time demands, regulatoryclassification, business considerations, and a combination thereof.

In some embodiments, the second level compatibility can comprisecompatibility of performing two assays concurrently on the automatedinstrument, the parameters selected from the group consisting of:regulatory classification, workflow incompatibility, businessconsiderations, and a combination thereof.

In some embodiments, the instrument prevents the concurrent performanceof incompatible assays within the same workstation when the firstcompatibility indexes are different. In some embodiments, the twodiscrete assay workflows are performed in the same workstation. In someembodiments, the instrument is prevented from concurrently performingassays with different second compatibility index values. In someembodiments, two assays have the same first level compatibility indexvalue and have different second level compatibility index values. Insome embodiments, the difference in the second level compatibility indexvalues can comprise a business reason. In some embodiments, thedifference in the second level compatibility index values can comprise aregulatory classification.

In some embodiments, if the assays are compatible, the method canfurther comprise one or more of the following (d) initiating anassay-specific sample preparation script on the instrument; (e)comparing identifying indicia on a consumable package to a set ofassay-specific identifying data stored on the instrument; (f) initiatingan assay-specific load cartridge script on the instrument; (g) comparinglevels of detectable signals fluorescence ratios in a loaded cartridgeto a set of assay-specific detectable signal data stored on theinstrument to determine whether the cartridge was successfully loaded;(h) initiating an assay-specific reaction script on the instrument; (i)initiating an assay-specific data analysis algorithm on the instrument;or (j) deriving a final call for the assay, based on one or moreassay-specific result algorithms or scripts.

In some embodiments, the assay protocol can comprise a reaction selectedfrom the group selected from: Polymerase Chain Reaction (PCR),Transcription Mediated Amplification (TMA), Oligonucleotide LigationAssay (OLA), Ligase Chain Reaction (LCR), Rolling Circle Amplification(RCA), Strand Displacement Amplification (SDA), and a hybridizationreaction.

Also presented herein is a system for performing an automated assay, thesystem comprising an automated instrument comprising a first workstationand a second workstation, each of the first and second workstationsconfigured to receive and processes a plurality of samples according toa plurality of different automated assay workflows, wherein eachdifferent automated assay workflow has an associated unique assaydefinition file or user-defined protocol file; a processor; a storagecapacity; and a program for performing an automated assay, the programcomprising instructions for determining whether two discrete assayworkflows are compatible or incompatible with each other for concurrentprocessing on the automated instrument; and performing the discreteassay workflows concurrently on the instrument when the assays arecompatible.

In some embodiments of the above system, the assay definition file oruser defined protocol file can comprise a first level compatibilityindex value, and wherein the determining step can comprise: (a)selecting a first assay from among a first list of available assays; and(b) evaluating which of a plurality of other available assays have anassay definition file comprising the same first level compatibilityindex value as the first assay, wherein the same first levelcompatibility index value is indicative of first-level compatibility.

In some embodiments of the above system, the evaluating step cancomprise (b1) identifying any assays which have first levelcompatibility index values different from the first compatibility indexvalue of the first assay; and (b2) providing a second list of secondassays, wherein the second list excludes any assay having a first levelcompatibility index value different from the first compatibility indexvalue of the first assay.

In some embodiments of the above system, each assay definition file cancomprise a second level compatibility index value, and wherein thedetermining step further can comprise (c) evaluating which of aplurality of other available assays have an assay definition filecomprising the same second level compatibility index value as the firstassay, wherein the same second level compatibility index value isindicative of second-level compatibility.

In some embodiments of the above system, the evaluating step cancomprise (c1) identifying any assays which have second levelcompatibility index values different from the second compatibility indexvalue of the first assay; and (c2) providing a second list of secondassays, wherein the second list excludes any assay having a second levelcompatibility index value different from the second compatibility indexvalue of the first assay.

In some embodiments of the above system, the first level compatibilitycan comprise compatibility of performing two assays concurrently at asingle workstation, the parameters selected from the group consistingof: incubation time, lysis time, reagent volume, reagent type,incubation temperature, lysis temperature, workstation time demands,regulatory classification, business considerations, and a combinationthereof.

In some embodiments of the above system, the second level compatibilitycan comprise compatibility of performing two assays concurrently on theautomated instrument, the parameters selected from the group consistingof: regulatory classification, workflow incompatibility, businessconsiderations, and a combination thereof.

In some embodiments of the above system, the instrument prevents theconcurrent performance of incompatible assays within the sameworkstation when the first compatibility indexes are different. In someembodiments, the two discrete assay workflows are performed in the sameworkstation. In some embodiments, the instrument is prevented fromconcurrently performing assays with different second compatibility indexvalues. In some embodiments, two assays have the same first levelcompatibility index value and have different second level compatibilityindex values. In some embodiments, the difference in the second levelcompatibility index values can comprise a business reason. In someembodiments, the difference in the second level compatibility indexvalues can comprise a regulatory classification.

In some embodiments of the above system, if the assays are compatible,the system can further comprise instructions for one or more of thefollowing (d) initiating an assay-specific sample preparation script onthe instrument; (e) comparing identifying indicia on a consumablepackage to a set of assay-specific identifying data stored on theinstrument; (f) initiating an assay-specific load cartridge script onthe instrument; (g) comparing levels of detectable signals in a loadedcartridge to a set of assay-specific detectable signal data stored onthe instrument to determine whether the cartridge was successfullyloaded; (h) initiating an assay-specific reaction script on theinstrument; (i) initiating an assay-specific data analysis algorithm onthe instrument; or (j) deriving a final call for the assay, based on oneor more assay-specific result algorithms or scripts.

In some embodiments of the above system, the assay protocol can comprisea reaction selected from the group selected from: Polymerase ChainReaction (PCR), Transcription Mediated Amplification (TMA),Oligonucleotide Ligation Assay (OLA), Ligase Chain Reaction (LCR),Rolling Circle Amplification (RCA), Strand Displacement Amplification(SDA), and a hybridization reaction.

In some embodiments of the above system, the system further can comprisea bar code reader. In some embodiments of the above system, theidentifying indicia can comprise a bar code.

Also presented herein is a method of performing a plurality ofcompatible discrete assays concurrently on a single automatedinstrument, the method comprising, for each discrete assay: providing anautomated instrument comprising a first workstation and a secondworkstation, each of the first and second workstations configured toreceive and processes a plurality of samples according to a plurality ofdifferent automated assay workflows, wherein each different automatedassay workflow has an associated unique assay definition file oruser-defined protocol file comprising a first level compatibility indexvalue and a second level compatibility index value; selecting a firstassay from among a first list of available assays; evaluating which of aplurality of other available assays have an assay definition file oruser-defined protocol file comprising the same first level compatibilityindex value as the first assay, wherein the same first levelcompatibility index value is indicative of compatibility for concurrentprocessing on the same workstation of the automated instrument;evaluating which of a plurality of other available assays have an assaydefinition file or user-defined protocol file comprising the same secondlevel compatibility index value as the first assay, wherein the samesecond level compatibility index value is indicative of compatibilityfor concurrent processing on the automated instrument; and performingthe discrete assay workflows concurrently on the instrument when theassays are compatible.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic drawing demonstrating a method of assigning first-and second-level compatibility index values to a particular assayworkflow or user defined protocol (UDP).

FIG. 2 is a schematic drawing demonstrating a method of identifyingfirst-level and second level compatibility between two assay protocolsaccording to one embodiment.

FIG. 3 is a schematic drawing demonstrating a method of selecting andperforming concurrent assay protocols according to one embodiment.

FIG. 4 is a schematic drawing that illustrates an automated instrumentwith independent workstations and a shared service according to oneembodiment.

FIG. 5 is a look up table to show rack and run compatibility accordingto one embodiment.

DETAILED DESCRIPTION

Automated diagnostic instruments are now able to carry out processingand testing of multiple samples in parallel. These devices canadvantageously be used in high throughput to facilitate the samplepreparation and testing. By way of example, automated diagnosticinstruments can prepare samples for nucleic acid amplification assays,and perform the amplification and detection. Depending on the type ofsamples and the type of assay, however, many times, assay protocols arenot compatible with each other on the same instrument, either because ofphysical constraints on the instrument, or for business reasons. Forexample, any two assay protocols may have different incubation times,lysis times, reagent volumes, reagent types, incubation temperatures,lysis temperatures, workstation time demands, or other parameters thatrender it impossible for the instrument to perform different assays insamples in a single workstation, or even on the same instrument. Inaddition to physical constraints, regulatory classifications andbusiness considerations are each factors which may prevent theinstrument from processing samples concurrently. In order to addressthis issue, users had to manually compare assay protocols on a chart ortable to determine whether they can be performed concurrently on thesame rack, or even on different racks of the same instrument. Suchmanual approaches can be error prone, as well as inefficient and laborintensive. Thus, there exists a great need for improved methods toidentify compatible assay protocols and prevent incompatible assayprotocols from being performed concurrently.

In accordance with the above, provided herein are methods and systemsfor performing an assay protocol on an automated instrument. In someembodiments of the present technology, such methods and systems canpermit the concurrent performance of discrete assay workflows on aninstrument when the assay workflows are compatible, and can prevent theconcurrent performance of incompatible assay protocols within the sameinstrument. The methods provided herein allow for improved reliabilityand ease of use when performing an assay on an automated instrument.

Accordingly, provided herein is a method of providing an automatedinstrument comprising a first workstation and a second workstation and acommon service that is shared by both workstations, each of the firstand second workstations configured to receive and processes a pluralityof samples according to a plurality of different automated assayworkflows, wherein each different automated assay workflow has anassociated unique assay definition or user-defined protocol file;determining whether two discrete assay workflows are compatible orincompatible with each other for concurrent processing on the automatedinstrument; and performing the discrete assay workflows concurrently onthe instrument when the assay protocols are compatible.

As used herein, the terms “workstation,” “rack” and like terms refer toan assembly that can hold a plurality of samples within an instrumentdesigned to process those samples together. Thus, two workflows whichcan be performed concurrently on the same rack are designated herein as“rack-compatible.”

Two workflows which can be performed concurrently on the same instrumentare designated herein as “run-compatible.” In certain embodiments, tworun-compatible workflows are not compatible on the same rack, but can beperformed on separate racks in the instrument. In certain embodiments,two run-compatible workflows are compatible on the same rack. In certainother embodiments, two run-incompatible workflows are compatible on thesame rack, but cannot, for any one of a variety of reasons, be performedconcurrently on the same instrument.

As used herein, the terms “workflow,” “assay workflow,” “assay,” “assayprotocol,” “test,” and like terms refer to a procedure for processing asample. In typical embodiments, a workflow can include samplepreparation steps, such as cell lysis, nucleic acid extraction, nucleicacid purification, nucleic acid digestion, nucleic acid modification,protein extraction, protein purification, and the like. Several methodsof nucleic acid extraction useful in the embodiments disclosed hereinare known in the art. Exemplary discussions of nucleic acid extractioncan be found, for example, in U.S. patent application Ser. No.12/172,214, filed Jul. 11, 2008, U.S. patent application Ser. No.12/172,208, filed Jul. 11, 2008, and U.S. patent application Ser. No.11/281,247, filed Nov. 16, 2005, all of which are incorporated herein byreference in their entirety. Likewise, exemplary discussions of proteinextraction can be found, for example, in U.S. Pat. Nos. 8,053,239 and6,864,100, both of which are incorporated herein by reference in theirentirety.

In some typical embodiments, a workflow can also include nucleic acidamplification reactions. In some typical embodiments, a workflow canfurther include data analysis procedures.

Accordingly, in certain embodiments, workflows are not directlycompatible with each other due to physical differences, such asincubation time, lysis time, reagent volume, reagent type, incubationtemperature, lysis temperature, workstation time demands, and the like.Each of these parameters place unique physical restraints on the motionand capacity of either the workstation itself or on a shared serviceresource within an automated instrument. For example, an RNA extractionprotocol, a DNA extraction protocol, and a protein extraction protocolmay each require different motions for a pipetting head on aninstrument, and therefore cannot be processed at the same time on thesame workstation. By way of another example, a PCR assay and an assaybased solely upon hybridization of detectable probes to a target mayrequire different temperature cycling and timing requirements, andtherefore cannot be processed at the same time. It will be appreciatedthat any physical, temporal or other limitation can present a reason forwhich two workflows are not directly compatible with each other.

In certain embodiments, incompatibility is driven by physical restraintson motion and capacity of a shared service resource within an automatedinstrument that is shared by two or more workstations. As illustrated inFIG. 4, two or more independent workstations can utilize a sharedresource. The shared resource can be, for example, a pipettor, a roboticarm, a single detector unit, or any other resource that is shared by twoor more workstations.

The physical, temporal or other parameters need not be identical betweenassays in order to indicate compatibility. Rather, parameters can fallwithin a range which confers compatibility of, for example, a sharedresource. Table 2 in Example 1 below provides an example for assays withparameters that vary within a range, yet still maintain compatibility,whereas assays with parameters outside any one range are no longercompatible.

In addition, workflows that are otherwise physically compatible on aninstrument can nonetheless be incompatible for other reasons. In certainembodiments, two workflows cannot be performed concurrently in order tocomply with regulatory restraints. For example, if one assay protocolhas been approved by a regulatory agency such as the United Stated Foodand Drug Administration (FDA), that agency may stipulate that the assayprotocol cannot be performed concurrently with an unapproved assayprotocol. Likewise, in certain embodiments, a manufacturer or user ofinstruments, consumable materials, or reagents may be under contractualrestrictions or other business limitations, under which two workflowscannot be performed concurrently on the same instrument. It will beappreciated that incompatibility can be determined for any reason forwhich a manufacturer or user determines that two workflows should beincompatible. The methods and systems provided herein make it possibleto identify compatible workflows and perform a plurality of compatibleworkflows on the same instrument at the same time.

As illustrated in FIG. 3, rack and run compatibility can be determinedby any of a number of workflow parameters. For example, parameters whichmay determine rack or run compatibility include, but are not limited to,reagent strip design, number and type of consumable reagents and thespecific processes performed during the workflow, such as nucleic acidextraction or full analysis of a nucleic acid sample after extraction.

Assay Definition Files

In embodiments of the methods and systems provided herein, eachdifferent automated assay workflow has an associated unique assaydefinition or user-defined protocol file. As used herein, the term assaydefinition file (ADF) refers to a file that provides at least some, andtypically all of the assay specific parameters for that workflow. Inaddition, an ADF can provide compatibility index values for a particularworkflow. In typical embodiments, the ADF can contain all of theinformation needed to run the assay on an automated instrument. Onefunction of the ADF is to provide a layer of independence between theinstrument and the assay. This independence provides the mechanism bywhich an instrument manufacturer or assay reagent manufacturer canrelease new assay protocols for an instrument without producing majorrevisions to the instrument software.

An ADF can comprise one or more of the components set forth in Table 1below. In particular, the ADF can include the two-level index values forrack and run compatibility.

TABLE 1 ADF parameters and settings Level-1 compatibility index valueLevel-2 compatibility index value Sample prep parameters Scripts usedfor sample prep, load cartridge, and PCR. Required consumable barcodesFill check thresholds PCR Protocol Script used to generate resultsThresholds used to generate results Parameters used to drive the dataanalysis engine within the instrument

Thus, in some embodiments of the methods and systems provided herein, ifthe assay protocols are compatible, the ADF can include instructions forperforming one or more of the following: initiating an assay-specificsample preparation script on the instrument; comparing identifyingindicia on a consumable package to a set of assay-specific identifyingdata stored on the instrument; initiating an assay-specific loadcartridge script on the instrument; comparing levels of detectablesignals in a loaded cartridge to a set of assay-specific detectablesignal data stored on the instrument to determine whether the cartridgewas successfully loaded; initiating an assay-specific reaction script onthe instrument; initiating an assay-specific data analysis algorithm onthe instrument; or deriving a final call for the assay, based on one ormore assay-specific result algorithms or scripts. The detectable signalsthat are compared during a load cartridge script can be any suitabledetectable signal that indicates proper loading. In typical embodiments,the detectable signal is fluorescence, and the ratio of fluorescence atvarious wavelengths in a sample or reagent can be compared to set ofpre-determined fluorescence data in order to determine whether thecartridge was properly loaded.

In some embodiments, the ADF can also comprise a reaction including, butnot limited to: Polymerase Chain Reaction (PCR), Transcription MediatedAmplification (TMA), Oligonucleotide Ligation Assay (OLA), Ligase ChainReaction (LCR), Rolling Circle Amplification (RCA), Strand DisplacementAmplification (SDA), and a hybridization reaction.

Example 5 below describes an exemplary use of an ADF file to run assayprotocols on an instrument.

Typically, when a new assay is made available to a customer, thecorresponding ADF is installed on the instrument. Once an ADF isinstalled on the instrument, that assay is then available for executionon the instrument. The instrument software can then use the index valuesto control addition of tests to a run worklist. If assay protocols sharethe same rack index value, then they are allowed to be in the worklistin contiguous positions in a single rack. If two assay protocols have adifferent run index, then they can not be in the same run worklist. Whena user selects the first assay to be included in a run, the softwarechecks the compatibility index values of all other assay protocolsavailable on the instrument and modifies the list of assay protocolsthat the user can select according to the rules listed above, therebyensuring that the customer does not choose incompatible assay protocols.

An ADF may be provided in any suitable format. For example, the ADFcould be provided by a manufacturer on a storage medium such as CD-ROMor USB key, or downloaded from the manufacturer and then transferred tothe terminal that controls the instrument. Multiple ADFs, each defininga distinct assay protocol, can thus be installed on the same instrument.Advantageously, the methods and systems provided herein make it possiblefor the system to identify assay protocols with the same compatibilityindex values, rather than force a user to consult a chart or table.

User Defined Protocols

In certain embodiments, assay parameters are determined by the user,rather than the manufacturer. These user defined protocols (UDP) canalso be assigned first-level and second-level compatibility index valuesto ensure compatibility with other commercially-developed assayprotocols. One of the benefits of the indexes and assay definition filesis that it provides a firewall between user defined assay protocols andcommercially-developed assay protocols that also covers compatibility.The index values can be used to set up unique controls for user definedprotocols which are different from the index values forcommercially-developed assay protocols. In the embodiment illustrated inFIG. 1, User Defined Protocols are represented by the boxes labeled asUDP and Extraction Only.

Thus, as illustrated in FIG. 1, first-level and second-levelcompatibility index values for a UDP can be assigned according tosimilar factors that determine compatibility for ADFs. Such factorsinclude, for example, the extraction kit and PCR type selected by theuser, reagent strip design, the number of MM (master mixes), and thespecific process (extraction versus full process). The UDP can thusinclude compatibility index values as part of the full code, since thereis no ADF provided by a manufacturer. An illustration of this process isset forth in Example 6 below.

It will be appreciated that new extraction kits, PCR assay types, andother reagents can be provided by a manufacturer with a file similar toan ADF. Thus, when such files are installed on an instrument, and a newUDP is created, the index values for one or more UDPs may be updatedaccordingly.

First Level Compatibility Index Value

In some embodiments, the assay definition or user defined protocol filecan comprise a first level compatibility index value. Typically, thefirst level compatibility index value refers to rack compatibility.However, in certain other embodiments, the first level compatibilityindex value refers to run compatibility and the second level index valuerefers to rack compatibility. Thus, the method can comprise (a)selecting a first assay protocol from among a first list of availableassay protocols; and (b) evaluating which of a plurality of otheravailable assay protocols have an assay definition file comprising thesame first level compatibility index value as the first assay. Intypical embodiments, two assay protocols having the same first levelcompatibility index value is indicative of first-level compatibility. Itwill be appreciated, however, that any suitable mechanism that canassign and identify compatibility values to individual assays can servein the methods and systems provided herein. Thus, in some embodiments,two assay protocols that are rack compatible may have different firstlevel index values. However, for convenience in this disclosure, twoassay protocols with first level compatibility are considered as havingthe same first level compatibility index value.

The list of available assay protocols can change as the user selects oneor more assay protocols to perform, and first level compatibility isevaluated. As such, the evaluating step (b) can comprise the steps of(b1) identifying any assay protocols which have first levelcompatibility index values different from the first compatibility indexvalue of the first assay; and (b2) providing a second list of secondassay protocols, wherein the second list excludes any assay having afirst level compatibility index value different from the firstcompatibility index value of the first assay.

In some embodiments, the first level compatibility can take intoconsideration any parameter that could prevent performance of two assayprotocols concurrently at a single workstation. Such parameters areknown to those of skill in the art, and can include, for example,physical parameters such as incubation time, lysis time, reagent volume,reagent type, incubation temperature, lysis temperature, workstationtime demands, and the like. Further, other parameters can includeconsiderations such as regulatory classification, businessconsiderations, and the like.

Second Level Compatibility Index Value

In some embodiments, the assay definition or user defined protocol filecan comprise a second level compatibility index value. Typically, thesecond level compatibility index value refers to run compatibility.However, in certain other embodiments, the second level compatibilityindex value refers to rack compatibility and the second level indexvalue refers to run compatibility. Thus, the method can comprise (c)evaluating which of a plurality of other available assay protocols havean assay definition file comprising the same second level compatibilityindex value as the first assay, wherein the same second levelcompatibility index value is indicative of second-level compatibility.In typical embodiments, two assay protocols having the same second levelcompatibility index value is indicative of second level compatibility.It will be appreciated, however, that any suitable mechanism that canassign and identify compatibility values to individual assays can servein the methods and systems provided herein. Thus, in some embodiments,two assay protocols that are run compatible may have different secondlevel index values. However, for convenience in this disclosure, twoassay protocols with second level compatibility are considered as havingthe same second level compatibility index value.

The list of available assay protocols can change as the user selects oneor more assay protocols to perform, and second level compatibility isevaluated. As such, the evaluating step (c) can comprise the steps of(c1) identifying any assay protocols which have second levelcompatibility index values different from the second compatibility indexvalue of the first assay; and (c2) providing a second list of secondassay protocols, wherein the second list excludes any assay having asecond level compatibility index value different from the secondcompatibility index value of the first assay.

In some embodiments, the second level compatibility can take intoconsideration any parameter that could prevent performance of two assayprotocols concurrently at a single workstation. Such parameters areknown to those of skill in the art, and can include, for example,physical parameters such as incubation time, lysis time, reagent volume,reagent type, incubation temperature, lysis temperature, workstationtime demands, and the like. Further, other parameters can includeconsiderations such as regulatory classification, businessconsiderations, and the like.

In some embodiments, the instrument prevents the concurrent performanceof incompatible assay protocols within the same workstation when thefirst compatibility indexes are different. In some embodiments, the twodiscrete assay workflows are performed in the same workstation. In someembodiments, the instrument is prevented from concurrently performingassay protocols with different second compatibility index values. Insome embodiments, two assay protocols have the same first levelcompatibility index value and have different second level compatibilityindex values. In some embodiments, the difference in the second levelcompatibility index values can comprise a business reason. In someembodiments, the difference in the second level compatibility indexvalues can comprise a regulatory classification.

It will be appreciated that the two-level index described above isexpandable from a two workflow system to larger numbers of workflowsthat are desired to run concurrently on an instrument, but may haveconstraints to run concurrently based on physical or businessconstraints. Thus, as illustrated in FIG. 3, additional workflows may beadded to a rack or multiple racks as needed, and the methods describedherein will ensure that compatibility among all assays is maintained.

Instruments and Systems

Also presented herein is a system for performing an automated assay, thesystem comprising an automated instrument comprising a first workstationand a second workstation, each of the first and second workstationsconfigured to receive and processes a plurality of samples according toa plurality of different automated assay workflows, and supported by asingle service resource. Each different automated assay workflowtypically comprises an associated unique assay definition file oruser-defined protocol file. The system also comprises a processor; astorage capacity; and a program for performing an automated assay, theprogram comprising instructions for determining whether two discreteassay workflows are compatible or incompatible with each other forconcurrent processing on the automated instrument; and performing thediscrete assay workflows concurrently on the instrument when the assaysare compatible.

Automated instruments which can perform multiple assay protocolsconcurrently are known to those of skill in the art. Exemplarydiscussions of typical automated instruments for use with the methodsprovided herein can be found, for example, in U.S. patent applicationSer. No. 12/173,023, filed Jul. 14, 2008, which is incorporated hereinby reference in its entirety.

It will be appreciated that the methods and systems described herein canapply to instruments that comprise 2, 3, 4 or more workstations whereinat least 2 of the workstations are supported by a common serviceresource. For example, an instrument with 4 workstations and a singlepipette head could still be compatibility controlled by the 2 indexconcept described herein.

As used herein, the terms storage capacity, storage device, storage andthe like can refer to any medium, device or means of storage ofinformation. Storage can include, but is not limited to, a disk drivedevice such as a hard drive, floppy disk, optical or magneto-opticaldisk, memory such as RAM or ROM chips, and any other medium used torecord or store data. In some embodiments, a storage capacity isconnected to a processor which sends information to be recorded on thestorage capacity after it is acquired. In specific embodiments, data isacquired by a system and is recorded on a storage capacity. In otherembodiments, data is acquired by a system and information is firstprocessed and the processed information is recorded on a storagecapacity.

The files and programs provided herein can be in any suitableprogramming language. In certain embodiments, the ADF utilizes XML as amechanism for formatting files. Further, in certain embodiments, ADFutilizes Python as a scripting language to provide a mechanism forexecuting result logic using common technologies available on theinstrument. It will be appreciated that any suitable file format andprogramming language can be utilized in the methods and systems providedherein. In certain embodiments, files can be encrypted to protectagainst the use of counterfeit reagents and to control specificparameter details on assay runs.

As used herein, an “input” can be, for example, data received from akeyboard, rollerball, mouse, voice recognition system or other devicecapable of transmitting information from a user to a computer. The inputdevice can also be a touch screen associated with the display, in whichcase the user responds to prompts on the display by touching the screen.The user may enter textual information through the input device such asthe keyboard or the touch-screen.

The invention is operational with numerous other general purpose orspecial purpose computing system environments or configurations.Examples of well-known computing systems, environments, and/orconfigurations that may be suitable for use with the invention include,but are not limited to, microcontrollers, personal computers, servercomputers, hand-held or laptop devices, multiprocessor systems,microprocessor-based systems, programmable consumer electronics, networkPCs, minicomputers, mainframe computers, distributed computingenvironments that include any of the above systems or devices.

As used herein, “instructions” refer to computer-implemented steps forprocessing information in the system. Instructions can be implemented insoftware, firmware or hardware and include any type of programmed stepundertaken by components of the system.

A “microprocessor” or “processor” may be any conventional generalpurpose single- or multi-core microprocessor such as a Pentium®processor, Intel® Core™, a 8051 processor, a MIPS® processor, or anALPHA® processor. In addition, the microprocessor may be anyconventional special purpose microprocessor such as a digital signalprocessor or a graphics processor. A “processor” may also refer to, butis not limited to, microcontrollers, field programmable gate arrays(FPGAs), application-specific integrated circuits (ASICs), complexprogrammable logic devices (CPLDs), programmable logic arrays (PLAs),microprocessors, or other similar processing devices.

The system is comprised of various modules as discussed in detailherein. As can be appreciated by one of ordinary skill in the art, eachof the modules comprises various sub-routines, procedures, definitionalstatements and macros. Each of the modules are typically separatelycompiled and linked into a single executable program. Therefore, thefollowing description of each of the modules is used for convenience todescribe the functionality of the preferred system. Thus, the processesthat are undergone by each of the modules may be arbitrarilyredistributed to one of the other modules, combined together in a singlemodule, or made available in, for example, a shareable dynamic linklibrary.

Certain embodiments of the system may be used in connection with variousoperating systems such as SNOW LEOPARD®, iOS®, LINUX, UNIX or MICROSOFTWINDOWS®.

Certain embodiments of the system may be written in any conventionalprogramming language such as assembly, C, C++, C#, BASIC, Pascal, orJava, and run under a conventional operating system.

In addition, the modules or instructions may be stored onto one or moreprogrammable storage devices, such as FLASH drives, CD-ROMs, hard disks,and DVDs. One embodiment includes a programmable storage device havinginstructions stored thereon.

In some embodiments of the above system, the system further can comprisea device for reading identifying indicia on reagent packaging. It willbe appreciated that any suitable device for reading identifying indiciacan be used in the systems provided herein. Likewise, any suitableidentifying indicia may be used that is compatible with the device onthe instrument. Examples include bar codes, QR codes, RFID tags, colorcodes and the like. In typical embodiments, the device can be a bar codereader, and the identifying indicia can comprise a bar code. Example 4below describes use of barcode labels to properly identify consumablereagents.

Advantages and Improvements

The methods and systems presented herein provide numerous advantagesover existing approaches. For example, the use of an ADF by amanufacturer for the distribution of an assay protocols provides amechanism for release of new or modified assay protocols on theinstrument platform without requiring a coordinated instrument softwareupdate. By eliminating the need for instrument software revisions, thisapproach provides a more direct path towards release for the assay.Additionally, as needed, the manufacturer can modify compatibilitybetween assay protocols to meet business or other needs without havingto revise the instrument software.

Compatibility has traditionally been controlled using a table or othermeans that is maintained within the system and requires an update toexpand menu. Using a two-level index does not require updating a tableor any other means in the software to expand menu. Further, users do notneed to have any specific knowledge about assay compatibility since theinstrument software controls which assay protocols are available to mixin a single run.

An additional advantage of using an ADF is that barcode information inthe ADF can be used to confirm that reagents are appropriately loadedonto the instrument, thereby preventing user error and the resultingloss of time and resources.

Having generally described this invention, a further understanding canbe obtained by reference to certain specific examples which are providedherein for purposes of illustration only, and are not intended to belimiting.

Example 1 Assigning First-Level and Second-Level Compatibility IndexValues for User Defined Protocols and Commercially-Supplied AssayProtocols

This example demonstrates the process of assigning first- andsecond-level compatibility index values to a particular assay workflowor user defined protocol (UDP).

An automated sample processor and analysis instrument has the ability torun two discrete sample processing workflows, or racks, concurrently(run compatible). However, there are certain actions within a sampleprocessing workflow that modified and still maintain compatibility(rack-compatible) as well as certain actions that render workflowsincompatible on the instrument in the same run (incompatible). Inaddition to physical limitations, there may be business requirements tokeep assay protocols from running together on an instrument.

To manage this range of performance demands, a two-level index wasgenerated that identifies rack-compatible and run-compatible assayprotocols. The index is assigned and maintained by the instrumentmanufacturer. The first level index implicates rack-compatibility, thatis, assay protocols with the same index value can run in the same rack.The second level index implicates run-compatibility, that is, assayprotocols which can be practiced in the second rack on an instrumentrelative to the assay in the first rack; by definition, rack-compatibleassay protocols are also run-compatible. If assay protocols do not sharea rack or run compatible index level, then the instrument is preventedfrom performing assay protocols on the instrument concurrently.

FIG. 1 illustrates an exemplary embodiment of this process. In theprocess shown in FIG. 1, run compatibility (second level compatibility)is indicated by protocols on the same vertical level. Rack compatibility(first level compatibility) is indicated by protocols on the samehorizontal level. Thus, for example, two samples must be in the same boxin the diagram to be in the same rack in a worklist. Boxes on the samehorizontal level share the same Level 2 compatibility index, that is,assay protocols from different boxes can be on separate racks inside thesame run, but not in the same rack.

As shown in FIG. 1, factors that determine compatibility are reagentstrip design, the number of MM (master mixes), the use of a UDP or ADF(user defined protocol versus assay definition file), and the specificprocess (extraction versus full process).

Table 2 below illustrates several parameters that can influencecompatibility. For example, in Table 2, cells with italic text highlightthe parameters in Assays 4 and 5 that break compatibility with GuardrailFamily A. Specifically, for Assay 4, aspiration height, lysistemperature, number of washes and magnet speed are outside of the limitsfor each parameter defined for Assays 1-3. Similarly, for Assay 5,aspiration height and lysis time are outside the limits for thoseparameters.

TABLE 2

Table 2 thus illustrates that physical, temporal or other parametersneed not be identical between assays in order to indicate compatibility.Rather, parameters can fall within a range which confers compatibilityof, for example, a shared resource.

Table 3 below is an example of a table that assigns rack and runcompatibility values for a set of assay protocols.

TABLE 3 Assay Level 1 Level 2 Protocol Workflow Type Index Index 1Extract DNA 1 1 2 UDP DNA 2 2 3 Family A 3 2 4 Family A 3 2 5 Family A 43 6 Extract RNA 5 1 7 Extract RNA 5 1 8 UDP RNA 6 2 9 Family B 7 2 10Family C 8 4

In Table 3, Families A, B, and C represent workflows that are notdirectly compatible with each other due to physical differences, such asincubation time, lysis time, reagent volume, reagent type, incubationtemperature, lysis temperature or workstation time demands. In thediagram and the table, families A and B are run compatible, meaning thata first workstation could practice tests in Family A (not B), and that asecond workstation could practice test in Family B (not A, if a B isselected for that workstation first). As shown in FIG. 1, Family C isneither rack- nor run-compatible with the other workflows.

In Table 3, three different Family A tests have a differentcompatibility index. While the workflows would indicate that they shouldbe physically compatible, there could be other reasons that themanufacture chooses not to practice them on in the instrument at thesame time. For example, when the manufacturer partners with a thirdparty company, it may be desirable to prevent the user to run bothmanufacturer-supplied and third party-supplied tests on the instrumentat the same time, even if the workflow of the test would allow it.

Example 2 Identification of Assay Compatibility

This example demonstrates identification of first-level and second-levelcompatibility between two assay protocols according to one embodiment.In the exemplary methods shown in FIG. 2, the compatibility between afirst and second assay is determined by comparing two levels ofcompatibility index values. In order to avoid running incompatibleassays concurrently, users had to manually compare assay protocols on achart or table to determine whether they can be performed concurrentlyon the same rack, or even on different racks of the same instrument. Anexample of such a look up table is shown in FIG. 5. Such manualapproaches can be error prone, as well as inefficient and laborintensive. This example provides an example of an automated method toidentify compatible assay protocols and prevent incompatible assayprotocols from being performed concurrently.

Assay Protocols on the Same Rack.

As described in the schematic shown in FIG. 2, a first assay is selectedby the user from a list of all available assay protocols. Based on userinput, the first-level (rack) compatibility index value for the selectedfirst assay is obtained from the assay definition file (ADF) for thefirst assay, or from the UDP if the selected assay is user-defined. Thatcompatibility index value is then compared to the first-levelcompatibility index value (obtained from the ADF or UDP for eachrespective assay) of each of the other available assay protocols. Allassay protocols are identified which share a first-level compatibilityindex value with the selected assay, and any non-compatible assayprotocols are excluded from further consideration.

Next, the system obtains the second-level (nm) compatibility index valuefor the selected first assay and compares the value to the second-levelcompatibility index value of all other remaining assay protocols. Allassay protocols are identified which share a second-level compatibilityindex value with the selected assay, and any non-compatible assayprotocols are excluded from further consideration. A list is thendisplayed which contains only first- and second-level compatible assayprotocols. The user selects a second assay from that list, and whenselection is complete, the system begins to perform the two assayprotocols concurrently on the same rack, or on separate racks ifdesired.

Assay Protocols on Separate Racks.

Alternatively, the system can identify and run assay protocols onseparate racks when they are not compatible to run together on the samerack. As described in the schematic shown in FIG. 2, a first assay isselected by the user from a list of all available assay protocols. Basedon user input, the first-level (rack) compatibility index value for theselected first assay is obtained from the assay definition file (ADF)for the first assay, or from the UDP if the selected assay isuser-defined. That compatibility index value is then compared to thefirst-level compatibility index value (obtained from the ADF or UDP foreach respective assay) of each of the other available assay protocols.If no assay protocols are identified which share a first-levelcompatibility index value with the selected assay, the system thenobtains the second-level (nm) compatibility index value for the selectedfirst assay and compares the value to the second-level compatibilityindex value of all other available assay protocols. All assay protocolsare identified which share a second-level compatibility index value withthe selected assay, and any non-compatible assay protocols are excludedfrom further consideration. A list is then displayed which contains onlyassay protocols which are compatible to run concurrently on separateracks. The user selects a second assay from that list, and whenselection is complete, the system begins to perform the two assayprotocols concurrently on separate racks.

No Other Compatible Assay Protocols.

In the event that the system does not identify other assay protocolswhich are either rack-compatible or run-compatible, the user can chooseto perform a single assay protocol, using one or multiple samples, onthe same or separate racks.

Example 3 Addition of Tests to a Run Worklist

This example demonstrates the process of preparing a run worklist,including identification of assay protocols which can run concurrentlyin the same worklist, either on the same or on separate racks.

A user has a predetermined number of samples, each of which must beassigned an assay protocol. As shown in FIG. 3, a blank worklist isprovided, setting forth a complete list of available assay protocols.The user selects a first test from the test list. Upon entry of the userselection, the system auto-excludes all protocols with a differentfirst-level compatibility index value, and displays a list of only thoseassay protocols that are not excluded. From the list of remainingprotocols, the user selects another protocol from the list. This processrepeats until all samples have been assigned an assay protocol, or untilthe first rack is full.

If the first rack is full, the system allows the user to begin selectingassay protocols for the second rack. The system displays all protocolswith the same level 2 (run compatible) index values as those in thefirst rack. The user then selects a protocol from that list of runcompatible protocols. Once a first selection has been made for thesecond rack, the system auto-excludes all protocols with a differentfirst-level compatibility index value, and displays a list of only thoseassay protocols that are not excluded. From the list of remainingprotocols, the user selects another protocol from the list. This processrepeats until all samples have been assigned an assay protocol, or untilthe second rack is full.

Example 4 Use of Barcodes

This example demonstrates the use of barcodes as identifying indicia forconsumable packaging.

Consumable reagents provided by a supplier include a barcode label thatthe instrument can read. When an assay is created, the expected barcodesare identified in the ADF. When an instrument run commences, theinstrument executes a catalog process, which confirms that the userloaded the proper consumables on the instrument deck. The barcode datastored in the ADF is used to provide this verification. If the barcodeis not read, the instrument alerts the user and waits for assistance inacquiring the barcode. If the barcode is read, but does not match thatexpected for the assay test that was requested by the user, then theinstrument alerts the user and waits for assistance in correcting thedifference by, for example, swapping reagents. The use of barcodes onthe reagents and barcode information in the ADF provides processassurance that the user has run the assay appropriately.

Example 5 Use of ADF to Run Assay Protocol on Instrument

This example demonstrates the use of an ADF to accurately run assayprotocols on an instrument.

The instrument first checks the ADF to determine the sample prep scriptneeded to complete the run. The script data is then combined with thesample prep parameters defined in the ADF and the sample preparationprocess is initiated.

Upon completion of sample prep, the instrument again checks the ADF andexecutes the loadcartridge script identified in the ADF.

When loadcartridge completes, the instrument looks in the ADF to findout the fluorescence ratios needed to determine if the cartridgesuccessfully loaded and compares those ratios with readings taken. Ifthe instrument determines that the cartridge was successfully loaded, itthen looks in the ADF to determine the PCR scripts to be used and PCRprotocol necessary. Once these values are retrieved, the instrumentbegins the PCR process.

Upon completion of PCR, the instrument retrieves the parameters neededto run the data analysis algorithms from the ADF and executes the dataanalysis.

When data analysis completes the instrument combines the values returnedfrom the data analysis engine with the result logic and result scriptidentified in the ADF to derive a final call for that particular test.

Example 6

Generation of UDP and Assignment of First-Level and Second-LevelCompatibility Index Values

This example demonstrates the creation of a UDP and assignment ofcompatibility index values to the UDP to accurately run assay protocolson an instrument.

A user generates a new UDP by responding to prompts on a touch-screendisplay, selecting the assay type, assay parameters and reagents for theprotocol. Factors that are selected include, for example, type ofextraction kit and PCR parameters. Specifically, selecting from severalavailable options, the user selects a particular reagent strip design, aparticular of MM, and the specific process (extraction versus fullprocess). The user elects to program a full process, and as such, theuser can further define cycle times, temperatures and other parametersfor PCR.

Following a process set forth in FIG. 1, the system assigns first-leveland second-level compatibility index values for the UDP according tosimilar factors that determine compatibility for ADFs. Based uponparameters including aspiration height, lysis temperature, lysis time,number of washes and magnet speed, the new UDP is assigned a first-levelindex value of ‘2’ and a second-level index value of ‘2.’

Thus, going forward, when the user adds protocols to a run worklist, theuser will be able to perform the new UDP concurrently with other ADFs orUDPs that have first and second level index values of 2 and 2,respectively.

It is to be understood that this invention is not limited to particularembodiments described, as such may, of course, vary. It is also to beunderstood that the terminology used herein is for the purpose ofdescribing particular embodiments only, and is not intended to belimiting.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which the embodiments belong. Although any methods andmaterials similar or equivalent to those described herein may also beused in the practice or testing of the embodiments, the preferredmethods and materials are now described.

The term “comprising” as used herein is synonymous with “including,”“containing,” or “characterized by,” and is inclusive or open-ended anddoes not exclude additional, unrecited elements or method steps.

It must be noted that as used herein and in the appended claims, thesingular forms “a,” “and,” and “the” include plural referents unless thecontext clearly dictates otherwise. Thus, for example, reference to “amethod” includes a plurality of such methods and equivalents thereofknown to those skilled in the art, and so forth.

All references cited herein including, but not limited to, published andunpublished applications, patents, and literature references, areincorporated herein by reference in their entirety and are hereby made apart of this specification. To the extent publications and patents orpatent applications incorporated by reference contradict the disclosurecontained in the specification, the specification is intended tosupersede and/or take precedence over any such contradictory material.

The steps of a method or algorithm described in connection with theembodiments disclosed herein may be embodied directly in hardware, in asoftware module executed by a processor, or in a combination of the two.A software module may reside in RAM memory, flash memory, ROM memory,EPROM memory, EEPROM memory, registers, hard disk, a removable disk, aCD-ROM, or any other form of storage medium known in the art. Anexemplary storage medium may be coupled to the processor such theprocessor can read information from, and write information to, thestorage medium. In the alternative, the storage medium may be integralto the processor. The processor and the storage medium may reside in anASIC. The ASIC may reside in a user terminal. In the alternative, theprocessor and the storage medium may reside as discrete components in auser terminal.

1. A method of performing an automated assay on a plurality of samples,said method comprising: providing an automated instrument comprising afirst workstation and a second workstation, each of said first andsecond workstations configured to receive and processes a plurality ofsamples according to a plurality of different automated assay workflows,wherein each different automated assay workflow has an associated uniqueassay definition or user-defined protocol file; determining whether twodiscrete assay workflows are compatible or incompatible with each otherfor concurrent processing on the automated instrument; and performingsaid discrete assay workflows concurrently on said instrument when saidassays are compatible.
 2. The method of claim 1, wherein said assaydefinition or user defined protocol file comprises a first levelcompatibility index value, and wherein said determining step comprises:(a) selecting a first assay from among a first list of available assays;and (b) evaluating which of a plurality of other available assays havean assay definition file comprising the same first level compatibilityindex value as said first assay, wherein the same first levelcompatibility index value is indicative of first-level compatibility. 3.The method of claim 2, wherein said evaluating step comprises: (b1)identifying any assays which have first level compatibility index valuesdifferent from the first compatibility index value of said first assay;and (b2) providing a second list of second assays, wherein said secondlist excludes any assay having a first level compatibility index valuedifferent from the first compatibility index value of said first assay.4. The method of claim 2, wherein each assay definition file comprises asecond level compatibility index value, and wherein said determiningstep further comprises: (c) evaluating which of a plurality of otheravailable assays have an assay definition file comprising the samesecond level compatibility index value as said first assay, wherein thesame second level compatibility index value is indicative ofsecond-level compatibility.
 5. The method of claim 4, wherein saidevaluating step comprises: (c1) identifying any assays which have secondlevel compatibility index values different from the second compatibilityindex value of said first assay; and (c2) providing a second list ofsecond assays, wherein said second list excludes any assay having asecond level compatibility index value different from the secondcompatibility index value of said first assay.
 6. The method of claim 2,wherein said first level compatibility comprises compatibility ofperforming two assays concurrently at a single workstation, saidparameters selected from the group consisting of: incubation time, lysistime, reagent volume, reagent type, incubation temperature, lysistemperature, workstation time demands, regulatory classification,business considerations, and a combination thereof.
 7. The method ofclaim 4, wherein said second level compatibility comprises compatibilityof performing two assays concurrently on said automated instrument, saidparameters selected from the group consisting of: regulatoryclassification, workflow incompatibility, business considerations, and acombination thereof.
 8. The method of claim 6, wherein said instrumentprevents the concurrent performance of incompatible assays within thesame workstation when the first compatibility indexes are different. 9.The method of claim 8, wherein said two discrete assay workflows areperformed in the same workstation.
 10. The method of claim 7, whereinsaid instrument is prevented from concurrently performing assays withdifferent second compatibility index values.
 11. (canceled) 12.(canceled)
 13. (canceled)
 14. The method of claim 1, wherein if saidassays are compatible, said method further comprises one or more of thefollowing: (d) initiating an assay-specific sample preparation script onthe instrument; (e) comparing identifying indicia on a consumablepackage to a set of assay-specific identifying data stored on theinstrument; (f) initiating an assay-specific load cartridge script onthe instrument; (g) comparing fluorescence ratios in a loaded cartridgeto a set of assay-specific fluorescence ratio data stored on theinstrument to determine whether said cartridge was successfully loaded;(h) initiating an assay-specific reaction script on the instrument; (i)initiating an assay-specific data analysis algorithm on the instrument;(j) deriving a final call for the assay, based on one or moreassay-specific result algorithms or scripts.
 15. The method of claim 14,wherein said assay protocol comprises a reaction selected from the groupselected from: Polymerase Chain Reaction (PCR), Transcription MediatedAmplification (TMA), Oligonucleotide Ligation Assay (OLA), Ligase ChainReaction (LCR), Rolling Circle Amplification (RCA), Strand DisplacementAmplification (SDA), and a hybridization reaction.
 16. A system forperforming an automated assay comprising: an automated instrumentcomprising a first workstation and a second workstation, each of saidfirst and second workstations configured to receive and processes aplurality of samples according to a plurality of different automatedassay workflows, wherein each different automated assay workflow has anassociated unique assay definition file or user-defined protocol file; aprocessor; a storage capacity; and a program for performing an automatedassay, said program comprising instructions for: determining whether twodiscrete assay workflows are compatible or incompatible with each otherfor concurrent processing on the automated instrument; and performingsaid discrete assay workflows concurrently on said instrument when saidassays are compatible.
 17. The system of claim 16, wherein said assaydefinition file or user defined protocol file comprises a first levelcompatibility index value, and wherein said determining step comprises:(a) selecting a first assay from among a first list of available assays;and (b) evaluating which of a plurality of other available assays havean assay definition file comprising the same first level compatibilityindex value as said first assay, wherein the same first levelcompatibility index value is indicative of first-level compatibility.18. The system of claim 17, wherein said evaluating step comprises: (b1)identifying any assays which have first level compatibility index valuesdifferent from the first compatibility index value of said first assay;and (b2) providing a second list of second assays, wherein said secondlist excludes any assay having a first level compatibility index valuedifferent from the first compatibility index value of said first assay.19. The system of claim 17, wherein each assay definition file comprisesa second level compatibility index value, and wherein said determiningstep further comprises: (c) evaluating which of a plurality of otheravailable assays have an assay definition file comprising the samesecond level compatibility index value as said first assay, wherein thesame second level compatibility index value is indicative ofsecond-level compatibility.
 20. The system of claim 19, wherein saidevaluating step comprises: (c1) identifying any assays which have secondlevel compatibility index values different from the second compatibilityindex value of said first assay; and (c2) providing a second list ofsecond assays, wherein said second list excludes any assay having asecond level compatibility index value different from the secondcompatibility index value of said first assay.
 21. The system of claim17, wherein said first level compatibility comprises compatibility ofperforming two assays concurrently at a single workstation, saidparameters selected from the group consisting of: incubation time, lysistime, reagent volume, reagent type, incubation temperature, lysistemperature, workstation time demands, regulatory classification,business considerations, and a combination thereof.
 22. (canceled) 23.(canceled)
 24. (canceled)
 25. (canceled)
 26. (canceled)
 27. (canceled)28. (canceled)
 29. The system of claim 16, wherein if said assays arecompatible, said method further comprises one or more of the following:(d) initiating an assay-specific sample preparation script on theinstrument; (e) comparing identifying indicia on a consumable package toa set of assay-specific identifying data stored on the instrument; (f)initiating an assay-specific load cartridge script on the instrument;(g) comparing fluorescence ratios in a loaded cartridge to a set ofassay-specific fluorescence ratio data stored on the instrument todetermine whether said cartridge was successfully loaded; (h) initiatingan assay-specific reaction script on the instrument; (i) initiating anassay-specific data analysis algorithm on the instrument; (j) deriving afinal call for the assay, based on one or more assay-specific resultalgorithms or scripts.
 30. The system of claim 29, wherein said assayprotocol comprises a reaction selected from the group selected from:Polymerase Chain Reaction (PCR), Transcription Mediated Amplification(TMA), Oligonucleotide Ligation Assay (OLA), Ligase Chain Reaction(LCR), Rolling Circle Amplification (RCA), Strand DisplacementAmplification (SDA), and a hybridization reaction.
 31. The system ofclaim 16, wherein said system further comprises a bar code reader. 32.(canceled)
 33. (canceled)